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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct...

Basic information

species Oryza sativa
transcript LOC_Os06g05180.2
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G448913_T01 (Zea mays), 5'ss of exon 6
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgact-tttgatccaaaaca---atgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| ||||||||||||||||||||||||||| ||| ||   |  |  |||| ||||||| |   ||    || || | || |  |   | | |   |||  |||  ||  ||   |||  |   |     |||   
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttcttttctaatttatctctgcttttagacccatt--ttctattttgtggaagacaggtta--

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgact-tttgatccaaaacaatgagtttcttttattttggtacctgtttct--ctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||| |||||||||||||||| ||| ||   |  |  |||| ||||||| |   | |  ||||| ||||   |  | | |||   |||  |||  ||  ||   |||  |   |     |||   
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttttttctaatttatctctgcttttagacccatt--ttctattttgtggaagacaggttat-

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 2
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgact-tttgatccaaaaca---atgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| ||||||||||||||||||||||||||| ||| ||   |  |  |||| | ||||| |   ||    || || | || |  |   | | |   |||  |||  ||  ||   |||  |   |     |||   
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgattatcggtttgtttcaaaatatatattgactttttcttttctaatttatctctgcttttagacccatt--ttctattttgttgaagacaggtta--

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 16
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttt----tgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||||||| | |||| ||||||||| |||||| |||||||||||||||| ||||| |||| ||| ||| |  | | |    ||||      | | |   || | |   | |  |   | |||   |||  | | |||  ||   |||| |||        |    
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCAAAGGCACAATACAATAGgtttgttccaaaatgtaaactgatttttttctacgctcttttctctctctaatttatctttgcttttagatccgtt--ttctatttcgtaacggcagattat--

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctct-ttgaacctgttgatttggtttcttaataattttgttcct-----
| ||| | || |||||||||||||||||||||||||||||||| ||| | ||| | || ||||| ||| ||||||| || || || | |||  |||| | ||  |   || || || | | ||| ||||||| ||  |||| |||   ||  |     | |  |  |  |||   |     ||   |||  ||||| |        
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGgtagg--acttacctt-gttgcaagacaatga-ttgattttctttcaatatgtagaaatatgcttgatatgt--gtagaaattaaaaatgtttttggtaacagaat

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgt--tagttgctgacttttgatccaaaac--aatgagtttcttttattttggtacctgtttctctttga-acctgttgattt-ggtttcttaataattttgttcct
||||| | ||||||||||| |||||||||||||| |||||||| ||| | ||| | || ||||| ||| ||||||| || || || | |||  |||| | ||  |||||  |  || ||        ||  |||||   |   ||  |||  |      || | ||||| |  | ||||    || || ||  |||   |      
TACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGCATCATAACAGgtagtagttattttctgttatgttgttacggaatgacccttactttctttatttagaaattatgtttgatatgttttgagaaaggcttttttgtaagggt------

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATA------Agttagttgc--tgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
| ||| | || |||||||||||||||||||||||||||||||| ||| | ||| | || ||||||||| | ||||| || || || | |||  |||| |      |||||||| |  ||  ||  | | ||| | ||||| ||  |||| |||   ||  ||||    | ||  | || |   |       |||| |||  | ||   
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgtagaagttagttaccttgtgttacgttgcaagataatga-ttaattttctttcaata--tgttgaaatatg--cttgatatgtgtagaaattaaaaatgctttt---

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct-----------------------------------------------------------
||||| | |||||||||||||||||||| |||||||||||||| ||| | ||||  || |||||  | ||||| || || || |||| |||  |||||| ||  |    ||   |||    |  |  |  |       |  ||| ||||    ||     | |   |  | | |  |  |   ||||  ||| | |||||                                                           
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaa--attgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgt-tagttgctgacttttgatccaaaacaatgagtttcttttattttg-----gtacctgtttctctttgaacctgt-tgatttggtttcttaataattttgttcct
||||||| | |||||||||||||||||||||||| |||||||| ||  || ||||||||| ||| |||||||| |  || ||  | | ||| || |||| ||   |    | |   |  |   | | ||| |   || | | | ||||     |||  ||| ||     |     || ||||||| |  |||  ||  ||       
TACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCTCAAGAGCACTACAATAGgtactgaaattcatagtatactgacagcaaagtaattgtgtgaatttgatggtgtagatgtgtcctcaggttgtagtctgatttgatagcttgctagatt-------

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagtt------gctgacttttgatccaaaacaatgagtttcttt-tattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||| ||  | ||||| || |||||  ||||||| || || || || |  ||  |||||| || | ||      | || || ||| |  | |||| | |  |       |      |||    |  | |||| | ||       || ||| |    ||||||||    
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttc----atgttttgtggggaattttgta---

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58690875|gb|CK079562.1|CK079562
EST:     GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAA                         TGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
genomic: GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgct ... catatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
EST: gi|2443004|gb|C74775.1|C74775
EST:     GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAA                         TGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
genomic: GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgct ... catatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 69 (downstream exon)
Score: 42

TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgct ... catatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA




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